Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Ontology Set Up

Jennifer Leigh Vendetti vendetti at stanford.edu
Mon Jan 29 05:16:42 PST 2018


Hi Abbie,

Thanks for letting us know. I disabled the download URL, but left your ontology metadata in place in BioPortal. Feel free to modify it in the future if you do find a source file.

Kind regards,
Jennifer


On Jan 24, 2018, at 4:48 PM, Ward, Abigail <Abigail_Ward at DFCI.HARVARD.EDU<mailto:Abigail_Ward at DFCI.HARVARD.EDU>> wrote:

Hi Jennifer,

Thank you for your response. At this time I have been unable to locate a source file for this ontology, however if I find one in the future I will update the submission.

Thanks!
Abbie

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: Friday, January 19, 2018 2:40 PM
To: Ward, Abigail <Abigail_Ward at DFCI.HARVARD.EDU<mailto:Abigail_Ward at DFCI.HARVARD.EDU>>
Cc: support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Ontology Set Up

Hello Abbie,


On Jan 19, 2018, at 11:23 AM, Ward, Abigail <Abigail_Ward at DFCI.HARVARD.EDU<mailto:Abigail_Ward at DFCI.HARVARD.EDU>> wrote:

Hello!


My name is Abbie Ward and I am one of the research coordinators at Dana-Farber.

For one of our RedCap projects, we would like to utilize the ICD-O ontology set. Our RedCap team advised that I registered for BioPortal, and created an ontology following the instructions. The page for it can be found here:

http://bioportal.bioontology.org/ontologies/ICD-O-3_1

It does not appear that the ontology is ready to be used. What additional steps should I take to ensure that we can use this in our database relatively soon?


I looked at the ontology submission you created in BioPortal. It appears that you specified the ontology should be loaded by our system from the following URL:

http://codes.iarc.fr/codegroup/2

This URL points to an HTML page, rather than an ontology source file. We handle ontologies in OWL, OBO, and SKOS formats. A typical URL for loading an ontology includes the exact path to the ontology source file, including the file name itself, e.g.:

http://www.example.com/my_ontology.owl

It’s unclear to me from looking at their site if they provide their ontology in any of the formats BioPortal is able to load. If you’re able to locate something in one of the above mentioned formats, we could further assist you in trying to get it into BioPortal.



Also, as this is a very well established ontology, is there somewhere else that it is located?


I don’t know of anything offhand, but perhaps other subscribed to this support list know more?

Kind regards,
Jennifer





The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20180129/4d2cb7a0/attachment-0001.html>


More information about the bioontology-support mailing list